Mikko Purmonen

University of Eastern Finland, Joensuu Campus
Supervisor: Juha Rouvinen
Funding: other
Date: 20/04/2005

Molecular Dynamics of Xylanases and Fab-fragments

Xylan is one of the main building materials of the plant cell wall hemicellulose of deciduous trees. Xylans are polysaccharides, which are formed from beta-1,4-linked xylopyranosidic units. The most important enzymes taking part to the degradation of xylan polymers are endo-1,4-beta-xylanases (E.C. 3.2.1.8). Endo-1,4-beta-xylanases degrade xylan to short xylo-oligosaccharides units of variable lengths. The most important protein families of xylanases are families 10 and 11 because of their commercial purposes in the paper-, pulp-, feed-, baking- and brewing industry.

The second research field in my studies are the Fab-fragments of IgG antibody. IgG is made of three distinct fragments: a distorted Y shape with two similar Fab-fragments containing at their tips identical antigen binding sites and with the constant Fc-fragment. The Fab-fragment connects the antigen binding fragment that recognizes male steroid hormone testosterone to Fc-fragment. It has been difficult to generate and develop antibodies with high affinity specificity for steroids and that is why it is necessary to study already existing immunoglobulins. Antibodies have many applications in practice and one of them is diagnostics.

Molecular dynamics (MD) is one tool of computational chemistry to study biological problems. With MD it is possible to study the thermal stabilities of the xylanases and Fab-fragments by increasing the kinetic energy by heating up the system. By following the conformational changes as a function of time, it is possible to follow the denaturation of proteins. The aim of the study is to improve the thermal stabilities of xylanases and Fab-fragments assisted by MD.